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Yorodumi- EMDB-27659: cryoEM map of de novo hallucinated homooligomer of C18-C6 symmetr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27659 | ||||||||||||
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Title | cryoEM map of de novo hallucinated homooligomer of C18-C6 symmetry, design HALC18-6_265. | ||||||||||||
Map data | EM map | ||||||||||||
Sample |
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Keywords | De novo protein design / Computational protein design / Machine learning / Hallucination / homo-oligomers / DE NOVO PROTEIN | ||||||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.31 Å | ||||||||||||
Authors | Wicky BIM / Milles LF / Courbet AC / Baker D | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Science / Year: 2022 Title: Hallucinating symmetric protein assemblies. Authors: B I M Wicky / L F Milles / A Courbet / R J Ragotte / J Dauparas / E Kinfu / S Tipps / R D Kibler / M Baek / F DiMaio / X Li / L Carter / A Kang / H Nguyen / A K Bera / D Baker / Abstract: Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination ...Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination to generate a wide range of symmetric protein homo-oligomers given only a specification of the number of protomers and the protomer length. Crystal structures of seven designs are very similar to the computational models (median root mean square deviation: 0.6 angstroms), as are three cryo-electron microscopy structures of giant 10-nanometer rings with up to 1550 residues and symmetry; all differ considerably from previously solved structures. Our results highlight the rich diversity of new protein structures that can be generated using deep learning and pave the way for the design of increasingly complex components for nanomachines and biomaterials. #1: Journal: BioRxiv / Year: 2022 Title: Hallucinating protein assemblies Authors: Wicky BIM / Milles LF / Courbet A / Baker D | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27659.map.gz | 117.6 MB | EMDB map data format | |
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Header (meta data) | emd-27659-v30.xml emd-27659.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27659_fsc.xml emd_27659_fsc_2.xml emd_27659_fsc_3.xml | 10.5 KB 5.9 KB 5.9 KB | Display Display Display | FSC data file |
Images | emd_27659.png | 54.4 KB | ||
Masks | emd_27659_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-27659.cif.gz | 4.8 KB | ||
Others | emd_27659_half_map_1.map.gz emd_27659_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27659 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27659 | HTTPS FTP |
-Validation report
Summary document | emd_27659_validation.pdf.gz | 769.8 KB | Display | EMDB validaton report |
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Full document | emd_27659_full_validation.pdf.gz | 769.4 KB | Display | |
Data in XML | emd_27659_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | emd_27659_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27659 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27659 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27659.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | EM map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27659_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_27659_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_27659_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : De novo hallucinated homooligomer of C18-C6 symmetry, design HALC...
Entire | Name: De novo hallucinated homooligomer of C18-C6 symmetry, design HALC18-6_265. |
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Components |
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-Supramolecule #1: De novo hallucinated homooligomer of C18-C6 symmetry, design HALC...
Supramolecule | Name: De novo hallucinated homooligomer of C18-C6 symmetry, design HALC18-6_265. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: HALC18-6_265
Macromolecule | Name: HALC18-6_265 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: NIKIPNPKDL SELLKKLGEG LKGLPNLKTL TLTLSNIELP EDADLSPGAE GLGEGLKGLP NLETLTFTIS NIKIPNPKD LSELLKKLGE GLKGLPNLKT LTLTLSNIEL PEDADLSPGA EGLGEGLKGL PNLETLTFTI S NIKIPNPK DLSELLKKLG EGLKGLPNLK ...String: NIKIPNPKDL SELLKKLGEG LKGLPNLKTL TLTLSNIELP EDADLSPGAE GLGEGLKGLP NLETLTFTIS NIKIPNPKD LSELLKKLGE GLKGLPNLKT LTLTLSNIEL PEDADLSPGA EGLGEGLKGL PNLETLTFTI S NIKIPNPK DLSELLKKLG EGLKGLPNLK TLTLTLSNIE LPEDADLSPG AEGLGEGLKG LPNLETLTFT IS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | |||||||||
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Buffer | pH: 8.4 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |